<div dir="auto">I’d check the documentation and the raw files in the run folder if you aren’t sure but The maker consensus models will have maker in the 2nd column and the augustus will have augustus in second column of gff (‘source’) </div><div dir="auto"><br></div><div dir="auto">You might need to adjust your grep to only take those with augustus in 2nd Col. you can do grep -P “\taugustus\t” to get those. </div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Fri, Nov 25, 2022 at 8:56 AM Alam,Elissa <<a href="mailto:elissaralam@ufl.edu">elissaralam@ufl.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Would that include all the gene models predicted by Augustus or only the ones that Maker retains after considering all ab initio gene predictions (SNAP + Augustus) and the EST evidence?</p>
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<p class="MsoNormal">Thanks a lot,</p>
<p class="MsoNormal">Elissar</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:jason.stajich@gmail.com" target="_blank">Jason Stajich</a><br>
<b>Sent: </b>Friday, November 25, 2022 11:51 AM<br>
<b>To: </b><a href="mailto:elissaralam@ufl.edu" target="_blank">Alam,Elissar</a><br>
<b>Cc: </b><a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<b>Subject: </b>Re: [maker-devel] Augustus predictions within MAKER2</p>
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<p class="MsoNormal">After you run the gff3_merge step you can <u></u><u></u></p>
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<p class="MsoNormal">grep augustus final.gff > augustus.gff3 <u></u><u></u></p>
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<p class="MsoNormal">On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <<a href="mailto:elissaralam@ufl.edu" target="_blank">elissaralam@ufl.edu</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hello,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model
based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?</p>
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<p class="MsoNormal">Thanks a million,</p>
<p class="MsoNormal">Elissar</p>
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<p class="MsoNormal">-- <u></u><u></u></p>
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<p class="MsoNormal">Jason Stajich<br>
<a href="mailto:jason.stajich@gmail.com" target="_blank">jason.stajich@gmail.com</a><u></u><u></u></p>
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</blockquote></div></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Jason Stajich<br><a href="mailto:jason.stajich@gmail.com" target="_blank">jason.stajich@gmail.com</a><br></div></div>